If you install python through system packages, you need to install pip modules through packages as well, or you'll mess up the system ones. If pip could overwrite the system installation, you could get instabilities if the system depends on them.

Due to this mess, there's a lot of parameters that are implied when you run pip on Ubuntu and Debian, e.g. to ignore whatever is installed by the system. This made it really difficult to create Docker images once pip 10.0 hit the market. Whenever you install something through pip, it'll ignore that pip is installed and pull it again, breaking the Ubuntu wrapper that depends on the old version.